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PR DOMAIN-CONTAINING PROTEIN 16; PRDM16

PR DOMAIN-CONTAINING PROTEIN 16; PRDM16

Alternative titles; symbolsMDS1/EVI1-LIKE GENE 1; MEL1HGNC Approved Gene Symbol: PRDM16Cytogenetic location: 1p36.32 Genomic coordinates (GRCh38): 1:3,069,20...

Alternative titles; symbols

  • MDS1/EVI1-LIKE GENE 1; MEL1

HGNC Approved Gene Symbol: PRDM16

Cytogenetic location: 1p36.32 Genomic coordinates (GRCh38): 1:3,069,202-3,438,620 (from NCBI)

▼ Cloning and Expression
The 3q21q26 syndrome represents a recurrent translocation, inversion, or insertion between the regions 3q21 and 3q26 and is associated with myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML) (Secker-Walker et al., 1995). The disorder is frequently characterized by trilineage dysplasia, in particular dysmegakaryocytopoiesis, and poor prognosis. A similar type of MDS/AML has been reported with the recurrent t(1;3)(p36;q21) translocation (Moir et al., 1984; Bloomfield et al., 1985; Welborn et al., 1987). Near the breakpoint at 1p36.3, Mochizuki et al. (2000) identified a novel gene, MEL1, that encodes a zinc finger protein that is highly homologous to MDS1/EVI1, a protein encoded by a splice variant of the EVI1 gene (165215). The 1,257-amino acid MEL1 protein shares 56% amino acid identity with MDS1/EVI1 and has a similar domain structure. The first 222 amino acids of MEL1 are highly homologous to the PR domain of MDS1 (600049), and the rest of the MEL1 sequence is homologous to EVI1. Following the N-terminal PR domain, MEL1 has a zinc finger DNA-binding domain, a proline-rich domain, a repressor domain, a second zinc finger DNA-binding domain, and a C-terminal acidic domain. Northern blot and RT-PCR analyses of various leukemia cell lines revealed a major 8-kb MEL1 transcript only in cells with t(1;3). In human tissues, RT-PCR showed MEL1 expression only in uterus and fetal kidney. On the basis of the positional relationship between the EVI1 and MEL1 genes in each translocation, Mochizuki et al. (2000) suggested that both genes are transcriptionally activated by the translocation of the 3q21 region with the ribophorin-1 gene (RPN1; 180470).

Using PCR, Nishikata et al. (2003) cloned an MEL1 splice variant encoding a short isoform that they designated MEL1S. Compared with the full-length MEL1 protein reported by Mochizuki et al. (2000), the deduced 1,073-amino acid MEL1S protein lacks part of the N-terminal PR domain. RT-PCR detected both transcripts in kidney. MEL1 and MEL1S had apparent molecular masses of 170 and 150 kD, respectively, and t(1;3)-positive leukemias expressed predominantly MEL1S protein.

In fetal and adult human hearts, Arndt et al. (2013) observed localization of PRDM16 in the nuclei of both cardiomyocytes and interstitial cells. At mouse embryonic day 13.5, Prdm16 was localized throughout the ventricular myocardium, including endocardium and epicardium. In the adult mouse, Prdm16 localization was predominantly restricted to the nuclei of cardiomyocytes. In zebrafish, RNA in situ hybridization revealed predominant expression of prdm16 in the brain and heart.

▼ Gene Structure
Nishikata et al. (2003) determined that the PRDM16 gene contains 17 coding exons and spans about 400 kb. Exon 1 and exon 2 contain 1 and 2 transcription start sites, respectively. Exon 4 contains an internal initiation codon for translation of the short PRDM16 isoform.

▼ Mapping
Using FISH, Mochizuki et al. (2000) mapped the PRDM16 gene to chromosome 1p36.3.

▼ Gene Function
Nishikata et al. (2003) showed that both MEL1 and MEL1S bound the same consensus sequence as EVI1 in vitro. Reporter gene assays revealed that MEL1S weakly activated transcription via its second DNA-binding domain, whereas MEL1 showed neither transcriptional activation nor repression. Overexpression of MEL1S blocked granulocytic differentiation induced by GCSF (CSF3; 138970) in Il3 (147740)-dependent murine myeloid cells, but MEL1 could not block differentiation. Nishikata et al. (2003) concluded that overexpression of MEL1S is a causative factor in the pathogenesis of myeloid leukemia.

Using RT-PCR, Shing et al. (2007) detected overexpression of transcripts encoding full-length PRDM16 and/or the short PRDM16 isoform (sPRDM16) in all 5 leukemias with 1p36 rearrangements examined compared with normal CD34 (142230)-positive cells. Overexpression of both PRDM16 and sPRDM16 was also found in a significant subset of AMLs with normal karyotype, but not in AMLs with translocations other than 1p36. The AMLs with 1p36 rearrangements had a relatively high prevalence of mutations in p53 (TP53; 191170), and the AMLs with normal karyotype had a relatively high prevalence of mutations in nucleophosmin (NPM1; 164040), which regulates TP53. Overexpression of sPRDM16 in mouse bone marrow induced AML with full penetrance, but only in the absence of p53. The mouse leukemias were characterized by multilineage cellular abnormalities and megakaryocyte dysplasia, similar to human AMLs with 1p36 translocations or NPM1 mutations. Overexpression of sPRDM16 increased the pool of hematopoietic stem cells in vivo and blocked myeloid differentiation and prolonged progenitor life span in vitro. Loss of p53 augmented the effects of sPRDM16 on stem cell number and induced immortalization of progenitors. Shing et al. (2007) concluded that sPRMD16 cooperates with disruption of the p53 pathway in induction of myeloid leukemia.

Seale et al. (2008) demonstrated by in vivo fate mapping that brown, but not white, fat cells arise from precursors that express MYF5 (159990), a gene previously thought to be expressed only in the myogenic lineage. They also demonstrated that the transcriptional regulator PRDM16 controls a bidirectional cell fate switch between skeletal myoblasts and brown fat cells. Loss of PRDM16 from brown fat precursors causes a loss of brown fat characteristics and promotes muscle differentiation. Conversely, ectopic expression of PRDM16 in myoblasts induced their differentiation into brown fat cells. PRDM16 stimulates brown adipogenesis by binding to PPAR-gamma (601487) and activating its transcriptional function. Finally, Prdm16-deficient brown fat displays an abnormal morphology, reduced thermogenic gene expression, and elevated expression of muscle-specific genes. Taken together, Seale et al. (2008) concluded that PRDM16 specifies the brown fat lineage from a progenitor that expresses myoblast markers and is not involved in white adipogenesis.

Tseng et al. (2008) demonstrated that BMP7 (112267) activates a full program of brown adipogenesis, including induction of early regulators of brown fat fate PRMD16 and PGC1A (604517), increased expression of the brown fat-defining marker uncoupling protein-1 (UCP1; 113730) and adipogenic transcription factors PPAR-gamma and CCAAT/enhancer-binding proteins (C/EBPs; see 116897), and induction of mitochondrial biogenesis via p38 mitogen-activated protein kinase (MAPK14; 600289), and PGC1-dependent pathways.

Kajimura et al. (2009) demonstrated that PRDM16 forms a transcriptional complex with the active form of C/EBP-beta (189965), acting as a critical molecular unit that controls the cell fate switch from myoblastic precursors to brown fat cells. Forced expression of PRDM16 and C/CEBP-beta was sufficient to induce a fully functional brown fat program in naive fibroblastic cells, including skin fibroblasts from mouse and man. Transplantation of fibroblasts expressing these 2 factors into mice gave rise to an ectopic fat pad with the morphologic and biochemical characteristics of brown fat. Like endogenous brown fat, this synthetic brown fat tissue acted as a sink for glucose uptake, as determined by positron emission tomography with fluorodeoxyglucose. Kajimura et al. (2009) concluded that the PRMD16-C/EBP-beta complex initiates brown fat formation from myoblastic precursors and may provide opportunities for the development of therapeutics for obesity and type 2 diabetes.

Ohno et al. (2013) demonstrated that euchromatic histine-lysine N-methyltransferase-1 (EHMT1; 607001) is an essential brown adipose tissue (BAT)-enriched lysine methyltransferase in the PRDM16 transcriptional complex and controls brown adipose cell fate. Loss of EHMT1 in brown adipocytes causes a severe loss of brown fat characteristics and induces muscle differentiation in vivo through demethylation of histone 3 lysine 9 (H3K9me2 and 3) of the muscle-selective gene promoters. Conversely, EHMT1 expression positively regulates the BAT-selective thermogenic program by stabilizing the PRDM16 protein. Notably, adipose-specific deletion of EHMT1 leads to a marked reduction of BAT-mediated adaptive thermogenesis, obesity, and systemic insulin resistance. Ohno et al. (2013) concluded that EHMT1 is an essential enzymatic switch that controls brown adipose cell fate and energy homeostasis.

▼ Molecular Genetics
In 17 of 18 patients with a deletion in chromosome 1p36 (see 607872) who showed evidence of heart muscle disease (left ventricular noncompaction or cardiomyopathy; see 615373), Arndt et al. (2013) aligned the regions of chromosomal loss and identified a shared deleted interval at chr1:3,224,674-3,354,772 bp (GRCh37) that involved only a single gene, PRDM16, specifically exons 4 to 17. Sequencing of PRDM16 in 75 LVNC probands identified 3 probands with heterozygous PRDM16 mutations (605557.0001-605557.0003) that were not present in 156 controls or in the 1000 Genomes Project database. Analysis by RNA-seq of 131 explanted heart biopsy samples from patients with dilated cardiomyopathy who underwent transplantation revealed 4 additional variants in the PRDM16 gene in 5 patients (see, e.g., 605557.0004-605557.0006), which were confirmed by Sanger sequencing of genomic DNA from peripheral blood and were not listed in the 1000 Genomes Project or detected in 6,400 controls of the Exome Sequencing Project.

▼ Animal Model
Transcriptional cofactors are essential to the regulation of transforming growth factor-beta (TGFB; 190180) superfamily signaling and play critical and widespread roles during embryonic development, including craniofacial development. Bjork et al. (2010) described the cleft secondary palate-1 (csp1) N-ethyl-N-nitrosourea-induced mouse model of nonsyndromic cleft palate (NSCP; see OFC1, 119530) that is caused by an intronic Prdm16 splicing mutation. Prdm16 encodes a transcriptional cofactor that regulates TGF-beta signaling, and its expression pattern is consistent with a role in palate and craniofacial development. The cleft palate appeared to be the result of micrognathia and failed palate shelf elevation due to physical obstruction by the tongue, resembling human Pierre Robin sequence (261800)-like cleft secondary palate.

Arndt et al. (2013) performed morpholino knockdown of the zebrafish ortholog of PRDM16 to recapitulate potential haploinsufficiency. They observed dose-dependent bradycardia with significantly reduced cardiac output compared to controls. Contractile impairment was efficiently rescued by wildtype human PRDM16 in a dose-dependent manner. There was a significant decrease in total cardiomyocyte numbers as well as significantly decreased cardiomyocyte proliferation in the hearts of morphant zebrafish compared to wildtype, with evidence for a concomitant increase in apoptosis. In addition, there was a significant reduction in coupling in morphant hearts; mean estimated conduction velocities from the outer curvature of the ventricle confirmed a significant reduction in impulse propagation velocities in morphant hearts compared to wildtype.

▼ ALLELIC VARIANTS ( 6 Selected Examples):

.0001 LEFT VENTRICULAR NONCOMPACTION 8
PRDM16, LYS702TER
In a female patient diagnosed with left ventricular noncompaction (LVNC8; 615373), Arndt et al. (2013) identified heterozygosity for a de novo c.2104A-T transversion in exon 9 of the PRDM16 gene, resulting in a lys702-to-ter (K702X) substitution. The patient, who was diagnosed at 12 years of age due to arrhythmias, showed mild to moderate left ventricular dysfunction and dilation in addition to LVNC. The mutation was not found in her unaffected parents, in 156 controls, or in the 1000 Genomes Project database. In zebrafish transgenic for the K702X mutation, dose-dependent bradycardia was observed and cardiac output was significantly reduced compared to controls. Contractile impairment was efficiently rescued by wildtype PRDM16 in a dose-dependent manner, but required a 10-fold excess of wildtype RNA compared to a morphant knockdown zebrafish. There was a significant decrease in total cardiomyocyte numbers as well as significantly decreased cardiomyocyte proliferation in the hearts of mutant zebrafish compared to wildtype, with evidence for a concomitant increase in apoptosis. In addition, there was a significant reduction in coupling in mutant hearts; mean estimated conduction velocities from the outer curvature of the ventricle confirmed a significant reduction in impulse propagation velocities in mutant hearts compared to wildtype.

.0002 LEFT VENTRICULAR NONCOMPACTION 8
PRDM16, 1-BP DUP, 1573C
In a male patient diagnosed with left ventricular noncompaction (LVNC8; 615373), Arndt et al. (2013) identified heterozygosity for a de novo 1-bp duplication (1573dupC) in exon 9 of the PRDM16 gene, causing a frameshift resulting in a premature termination codon (Arg525ProfsTer79). The mutation was not found in his unaffected parents or sister, in 156 controls, or in the 1000 Genomes Project database. The patient presented at 33 years of age with severe biventricular heart failure with systolic and diastolic dysfunction, secondary pulmonary hypertension, and dilation of both atria and ventricles. He received a biventricular intracardiac defibrillator.

.0003 LEFT VENTRICULAR NONCOMPACTION 8
PRDM16, ASN816SER
In a male patient diagnosed with left ventricular noncompaction (LVNC8; 615373), Arndt et al. (2013) identified heterozygosity for a c.2447A-G transition in exon 9 of the PRDM16 gene, resulting in an asn816-to-ser (N816S) substitution at highly conserved residue. The mutation was not found in his unaffected parents, in 156 controls, or in the 1000 Genomes Project database. The patient underwent reconstruction of a dysplastic mitral valve due to grade 3 mitral insufficiency at 11 years of age, at which time the left atrium and ventricle were enlarged with preserved cardiac function. Histology of a left ventricular biopsy taken at cardiac surgery showed increased interstitial fibrosis and myocyte disarray.

.0004 RECLASSIFIED - VARIANT OF UNKNOWN SIGNIFICANCE
PRDM16, VAL1101MET
This variant, formerly titled CARDIOMYOPATHY, DILATED, 1LL, has been reclassified based on the report of Lek et al. (2016).

In 2 patients with dilated cardiomyopathy (CMD1LL; see 615373) who underwent heart transplantation, Arndt et al. (2013) identified heterozygosity for a c.3301G-A transition in exon 15 of the PRDM16 gene, resulting in a val1101-to-met (V1101M) substitution at a conserved residue in the C terminus, within a sequence that mediates interaction with SKI (164780) and regulation of TGFB (see 190180) signaling.

Lek et al. (2016) noted that the V1101M variant has a high allele frequency (0.0256) in the South Asian population in the ExAC database, suggesting that it is not pathogenic.

.0005 CARDIOMYOPATHY, DILATED, 1LL
PRDM16, PRO291LEU
In a patient with dilated cardiomyopathy (CMD1LL; see 615373) who underwent heart transplantation, Arndt et al. (2013) identified heterozygosity for a c.872C-T transition in exon 6 of the PRDM16 gene, resulting in a pro291-to-leu (P291L) substitution at a highly conserved residue in a zinc finger domain.

.0006 CARDIOMYOPATHY, DILATED, 1LL
PRDM16, LEU887PRO
In a patient with dilated cardiomyopathy (CMD1LL; see 615373) who underwent heart transplantation, Arndt et al. (2013) identified heterozygosity for a c.2660T-C transition in exon 9 of the PRDM16 gene, resulting in a leu887-to-pro (L887P) substitution at a highly conserved residue in the C terminus, within a sequence that mediates interaction with SKI (164780) and regulation of TGFB (see 190180) signaling.

Tags: 1p36.32

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